The objective of this research is to determine if the radiobiological effectiveness (RBE) values used presently in proton radiotherapy are accurate and well understood throughout the irradiated volume to provide the most efficacious treatment. If these values are underestimated this means that patients treated with protons could be receiving higher doses than required in the tumor area as well as in the healthy tissue surrounding the target area. These values could be affected by the production of secondary particles as well as recoil nuclei due to proton interactions. In order to determine this, Monte Carlo simulations using unique nuclear data libraries and intermediate energy nuclear modeling codes will be performed and several circumstances of clinical relevance tested. In addition to determining the proton RBE and spatial variation, we will investigate the RBE of ions such as 12C that present several advantages for radiotherapy. In recent years, the interest in using such kinds of ions for therapy have increased.